Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001991.1 Hibiscus syriacus cultivar Beakdansim tig00004072_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2373627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 13
Found at i:1021375 original size:55 final size:55
Alignment explanation
Indices: 1021244--1021468 Score: 337
Period size: 55 Copynumber: 4.1 Consensus size: 55
1021234 CTCCCTATTG
* * *
1021244 CTTCCACGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGAC-C-CACAAT
1 CTTCAACGATCGCGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCGAACAAT
* *** *
1021297 CTTTATTAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
1 CTTCAACGATCGCGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCGAACAAT
* *
1021352 CTTCAACGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCAAACAAT
1 CTTCAACGATCGCGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCGAACAAT
*
1021407 CTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
1 CTTCAACGATCGCGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCGAACAAT
1021462 CTTCAAC
1 CTTCAAC
1021469 AAATGGGTTC
Statistics
Matches: 152, Mismatches: 18, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
53 39 0.26
54 1 0.01
55 112 0.74
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (55 bp):
CTTCAACGATCGCGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCGAACAAT
Found at i:1021447 original size:110 final size:108
Alignment explanation
Indices: 1021244--1021468 Score: 378
Period size: 110 Copynumber: 2.1 Consensus size: 108
1021234 CTCCCTATTG
* * * **
1021244 CTTCCACGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATCTTTATTAATCG
1 CTTCAACGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCAACAATCTTCAACAATCG
1021309 CGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
66 CGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
*
1021352 CTTCAACGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACTCAAACAATCTTCAACGAT
1 CTTCAACGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGAC-C-AACAATCTTCAACAAT
1021417 CGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
64 CGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
1021462 CTTCAAC
1 CTTCAAC
1021469 AAATGGGTTC
Statistics
Matches: 109, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
108 45 0.41
109 1 0.01
110 63 0.58
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (108 bp):
CTTCAACGATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCAACAATCTTCAACAATCG
CGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAAT
Found at i:1021486 original size:55 final size:53
Alignment explanation
Indices: 1021317--1022078 Score: 393
Period size: 51 Copynumber: 14.5 Consensus size: 53
1021307 CGCGTCTGCC
* * * *
1021317 CCCTATTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACGAT-CGTGTCTGCC
1 CCCTATTTCTTCAGGGAGTATAGA-ACTCGAAC-ATCTTCAACAATGGGT-TC-GCT
* * * * * *
1021372 CCCTATATCTTCAGAGAGTATA-AGACTCAAACAATCTTCAACGATCGCG-TCTGCC
1 CCCTATTTCTTCAGGGAGTATAGA-ACTCGAAC-ATCTTCAACAAT-GGGTTC-GCT
*
1021427 CCCTATTTCTTCAGAGAGTATA-AGACTCGAACAATCTTCAACAAATGGGTTCGCT
1 CCCTATTTCTTCAGGGAGTATAGA-ACTCGAAC-ATCTTCAAC-AATGGGTTCGCT
* * *
1021482 CCCTATTTC-TCTAGGGAGTATGGAACTCAGACATATTCTTC-A-AACGGGTTCGCT
1 CCCTATTTCTTC-AGGGAGTATAGAACTC-GA-ACA-TCTTCAACAATGGGTTCGCT
** * *
1021536 CCCCCTTTC-TCTAGGGAGTATAGAACTCGAACATCTTC-A-AACGGGTTCACT
1 CCCTATTTCTTC-AGGGAGTATAGAACTCGAACATCTTCAACAATGGGTTCGCT
* * ***
1021587 CCCTCTTTCTTTAGGGAGTATAGAACTCGAACATC-TCTTTAA-GGGTTCGCT
1 CCCTATTTCTTCAGGGAGTATAGAACTCGAACATCTTCAACAATGGGTTCGCT
* *
1021638 CCCTCTTTC-TCTAGGGAGTATGGAACTCGAACATCTTCAAC--TGGGTTCGCT
1 CCCTATTTCTTC-AGGGAGTATAGAACTCGAACATCTTCAACAATGGGTTCGCT
* * * ** * *
1021689 CCCTCTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCT
1 CCCTATTTCTTCAGGGAGTATAGAACTCGAACATCTTCAAC-AATGGGTTCGCT
* * * * ** *
1021743 CCTTCTCTCTTTAAAGAGTATAGAACTCGAACATCTTC-A-AACGGGTTCGCT
1 CCCTATTTCTTCAGGGAGTATAGAACTCGAACATCTTCAACAATGGGTTCGCT
* * * * * * * *
1021794 CCTTCTTTCATT-AAGGAGTATGGAACTCGGATATCTTC-AC-ACGGGTTCACT
1 CCCTATTTC-TTCAGGGAGTATAGAACTCGAACATCTTCAACAATGGGTTCGCT
* * *
1021845 CCCTCTTTC-TCTAGGGAGTATGGAACTC-AGACATCTCTTC-A-AACGGGTTCGCT
1 CCCTATTTCTTC-AGGGAGTATAGAACTCGA-ACA--TCTTCAACAATGGGTTCGCT
* * * * * *
1021898 CCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTTC-A-AACGGGTTCGCT
1 CCCTATTTCTTCAGGGAGTATAGAACTCGAACATCTTCAACAATGGGTTCGCT
* * * * * * * * *
1021949 CCTTCTTTCTTTAAGGAGTATAGAAATCGCATATCTTC-AC-ACGAGTTCGCT
1 CCCTATTTCTTCAGGGAGTATAGAACTCGAACATCTTCAACAATGGGTTCGCT
** * * * * *
1022000 CATTCTTTC-TCTAGGGAGTATGGAACTCGGACATCTTC-A-AACGGGTTCGAT
1 CCCTATTTCTTC-AGGGAGTATAGAACTCGAACATCTTCAACAATGGGTTCGCT
* * *
1022051 CCCTCTCTC-TCTAGGGAGTATGGAACTC
1 CCCTATTTCTTC-AGGGAGTATAGAACTC
1022079 AAATAATCTT
Statistics
Matches: 604, Mismatches: 71, Indels: 68
0.81 0.10 0.09
Matches are distributed among these distances:
49 1 0.00
50 4 0.01
51 333 0.55
52 11 0.02
53 44 0.07
54 80 0.13
55 114 0.19
56 9 0.01
57 8 0.01
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (53 bp):
CCCTATTTCTTCAGGGAGTATAGAACTCGAACATCTTCAACAATGGGTTCGCT
Found at i:1021595 original size:51 final size:51
Alignment explanation
Indices: 1021468--1022078 Score: 674
Period size: 51 Copynumber: 11.8 Consensus size: 51
1021458 CAATCTTCAA
* * *
1021468 CAAATGGGTTCGCTCCCTATTTCTCTAGGGAGTATGGAACTCAGACATATTCTT
1 CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC-GA-ACA-TCTT
* *
1021522 CAAACGGGTTCGCTCCCCCTTTCTCTAGGGAGTATAGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTT
* * *
1021573 CAAACGGGTTCACTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCT
1 CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCT-T
**
1021625 TTAA-GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTT
* * *
1021675 C-AACTGGGTTCGCTCCCTCTTTCT-TCAGGGAGTATAGAACTCAAAAATCTTCTT
1 CAAAC-GGGTTCGCTCCCTCTTTCTCT-AGGGAGTATGGAACTC--GAA-CATCTT
** * * * ** *
1021729 CTTACGGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTT
* * * *
1021780 CAAACGGGTTCGCTCCTTCTTTCAT-TAAGGAGTATGGAACTCGGATATCTT
1 CAAACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTATGGAACTCGAACATCTT
* *
1021831 CACACGGGTTCACTCCCTCTTTCTCTAGGGAGTATGGAACTC-AGACATCTCTT
1 CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGA-ACA--TCTT
* * *
1021884 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATGGAACTCGAACATCTT
1 CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTT
* * * * * * *
1021935 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAAATCGCATATCTT
1 CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTT
* * ** *
1021986 CACACGAGTTCGCTCATTCTTTCTCTAGGGAGTATGGAACTCGGACATCTT
1 CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTT
* *
1022037 CAAACGGGTTCGATCCCTCTCTCTCTAGGGAGTATGGAACTC
1 CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC
1022079 AAATAATCTT
Statistics
Matches: 481, Mismatches: 61, Indels: 33
0.84 0.11 0.06
Matches are distributed among these distances:
49 2 0.00
50 3 0.01
51 341 0.71
52 8 0.02
53 48 0.10
54 76 0.16
55 3 0.01
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.32
Consensus pattern (51 bp):
CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACATCTT
Found at i:1022518 original size:36 final size:36
Alignment explanation
Indices: 1022460--1022649 Score: 238
Period size: 36 Copynumber: 5.2 Consensus size: 36
1022450 ACTCTTCTGA
* * **
1022460 GAAGGCTTAAAATGGATCTGCTTCACTACTT-TTTGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTA-TTCTCCGGT
* * *
1022497 GAAGACTTAAGATGGTTTGCTTCACTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
1022533 GAAGACTTATGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
1022569 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
*
1022605 GAAGGCTTCAGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
1022641 GAAGGCTTA
1 GAAGGCTTA
1022650 GGATTGACTT
Statistics
Matches: 136, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
35 1 0.01
36 122 0.90
37 13 0.10
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
Found at i:1027500 original size:21 final size:21
Alignment explanation
Indices: 1027455--1027613 Score: 209
Period size: 21 Copynumber: 7.6 Consensus size: 21
1027445 CCATGTGATG
* *
1027455 TGGTCTTCTCGTCTTTACGAA
1 TGGTCTTCTCGTCTTGATGAA
1027476 -GGTCTTCTCGTCGTT-ATGAA
1 TGGTCTTCTCGTC-TTGATGAA
*
1027496 AGGTCTTCTCGTCTTGATGAA
1 TGGTCTTCTCGTCTTGATGAA
1027517 TGGTCTTCTCGTCTTGATGAA
1 TGGTCTTCTCGTCTTGATGAA
*
1027538 TGGCCTTCTCGTCTTGATGAA
1 TGGTCTTCTCGTCTTGATGAA
1027559 TGG-CATTCTCGTCTTGATGAA
1 TGGTC-TTCTCGTCTTGATGAA
*
1027580 T-GACATTCTCGTCTTGATGAA
1 TGGTC-TTCTCGTCTTGATGAA
*
1027601 TGCTCTTCTCGTC
1 TGGTCTTCTCGTC
1027614 CTTGGTACAA
Statistics
Matches: 127, Mismatches: 5, Indels: 12
0.88 0.03 0.08
Matches are distributed among these distances:
20 20 0.16
21 106 0.83
22 1 0.01
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (21 bp):
TGGTCTTCTCGTCTTGATGAA
Found at i:1032298 original size:20 final size:21
Alignment explanation
Indices: 1032273--1032324 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1032263 TTTTCCCAAT
*
1032273 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1032293 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1032314 TCGCAATGCGA
1 TCGCAATGCGA
1032325 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1032338 original size:20 final size:20
Alignment explanation
Indices: 1032313--1032420 Score: 101
Period size: 20 Copynumber: 5.3 Consensus size: 20
1032303 AATTGGGAAA
1032313 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1032333 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1032353 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1032374 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * * *
1032394 TTCACAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
*
1032414 TTCGCAA
1 ATCGCAA
1032421 CGTGATTTAC
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.03
20 56 0.77
21 13 0.18
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1032421 original size:20 final size:20
Alignment explanation
Indices: 1032375--1032427 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1032365 TAATACAAAA
*
1032375 TCGCAACGAGATACTGACTT
1 TCGCAACGAGATTCTGACTT
* *
1032395 TCACAACGCGATTCTGACTT
1 TCGCAACGAGATTCTGACTT
*
1032415 TCGCAACGTGATT
1 TCGCAACGAGATT
1032428 TACATAGCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (20 bp):
TCGCAACGAGATTCTGACTT
Found at i:1032990 original size:19 final size:19
Alignment explanation
Indices: 1032940--1032995 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
1032930 TTCGAGAATG
1032940 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
1032960 ACTATCACAACGCGAAATA
1 AAAATCGCAACGCGAAATA
*
1032979 AAAATCGTAACGCGAAA
1 AAAATCGCAACGCGAAA
1032996 CCAAAGTCGC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1033072 original size:33 final size:33
Alignment explanation
Indices: 1033035--1033122 Score: 149
Period size: 33 Copynumber: 2.6 Consensus size: 33
1033025 GTTGCGATTT
1033035 TCATTTCGCGTTGCGATTCTCTCGCCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGCCGCGATAG
**
1033068 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGCCGCGATAG
1033101 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1033123 ATTATCTCGT
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
33 37 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.28, G:0.23, T:0.38
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGCCGCGATAG
Found at i:1033124 original size:20 final size:19
Alignment explanation
Indices: 1033002--1033147 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
1032992 GAAACCAAAG
* *
1033002 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
*
1033021 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
1033040 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
* **
1033056 TCGC--CGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
1033073 TCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
1033089 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
1033106 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTCTCATT
* *
1033126 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTCTCATT
1033146 TC
1 TC
1033148 AACCAAAAGA
Statistics
Matches: 101, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
14 18 0.18
16 5 0.05
17 5 0.05
19 42 0.42
20 30 0.30
21 1 0.01
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTCTCATT
Found at i:1034253 original size:20 final size:21
Alignment explanation
Indices: 1034228--1034286 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
1034218 GGCTGCTGGA
1034228 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
1034248 AACCGGTTCTGACCGG-TTTC
1 AACCGGTTCTAACCGGTTTTC
*
1034268 AACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
1034287 GACCGGTCCG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:1034264 original size:10 final size:10
Alignment explanation
Indices: 1034249--1034337 Score: 50
Period size: 10 Copynumber: 9.3 Consensus size: 10
1034239 CCGGTTTTCA
1034249 ACCGGTTCTG
1 ACCGGTTCTG
*
1034259 ACCGGTT-TCA
1 ACCGGTTCT-G
1034269 ACCGGTTC-G
1 ACCGGTTCTG
1034278 AACCGGTT-TG
1 -ACCGGTTCTG
*
1034288 ACCGG-TCCG
1 ACCGGTTCTG
*
1034297 AACCGGTT-TA
1 -ACCGGTTCTG
1034307 ACCGG-TCTG
1 ACCGGTTCTG
*
1034316 AACCGGGT-TG
1 -ACCGGTTCTG
1034326 ACCGG-TCTG
1 ACCGGTTCTG
1034335 ACC
1 ACC
1034338 CGACCCGACT
Statistics
Matches: 62, Mismatches: 6, Indels: 23
0.68 0.07 0.25
Matches are distributed among these distances:
8 3 0.05
9 23 0.37
10 34 0.55
11 2 0.03
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:1034293 original size:19 final size:20
Alignment explanation
Indices: 1034228--1034335 Score: 104
Period size: 19 Copynumber: 5.6 Consensus size: 20
1034218 GGCTGCTGGA
1034228 AACCGGTT-T-AACCGGTTTT
1 AACCGGTTCTGAACCGG-TTT
1034247 CAACCGGTTCTG-ACCGGTTT
1 -AACCGGTTCTGAACCGGTTT
1034267 CAACCGGTTC-GAACCGGTTT
1 -AACCGGTTCTGAACCGGTTT
* *
1034287 GACCGG-TCCGAACCGGTTT
1 AACCGGTTCTGAACCGGTTT
*
1034306 AACCGG-TCTGAACCGGGTT
1 AACCGGTTCTGAACCGGTTT
*
1034325 GACCGG-TCTGA
1 AACCGGTTCTGA
1034336 CCCGACCCGA
Statistics
Matches: 79, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.03
19 42 0.53
20 29 0.37
21 6 0.08
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.26
Consensus pattern (20 bp):
AACCGGTTCTGAACCGGTTT
Found at i:1034300 original size:29 final size:28
Alignment explanation
Indices: 1034248--1034321 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
1034238 ACCGGTTTTC
*
1034248 AACCGGTTCTGACCGGTTTCAACCGGTTCG
1 AACCGGTT-TGACCGGTTCCAACCGGTT-G
*
1034278 AACCGGTTTGACCGG-TCCGAACCGGTTT
1 AACCGGTTTGACCGGTTCC-AACCGGTTG
*
1034306 AACCGGTCTGAACCGG
1 AACCGGTTTG-ACCGG
1034322 GTTGACCGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 11 0.28
29 20 0.51
30 8 0.21
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (28 bp):
AACCGGTTTGACCGGTTCCAACCGGTTG
Found at i:1034319 original size:38 final size:39
Alignment explanation
Indices: 1034259--1034332 Score: 116
Period size: 38 Copynumber: 1.9 Consensus size: 39
1034249 ACCGGTTCTG
*
1034259 ACCGGTTTCAACCGGTTCGAACCGGTTTGACCGGTCCGA
1 ACCGGTTTCAACCGGTTCGAACCGGGTTGACCGGTCCGA
1034298 ACCGGTTT-AACCGG-TCTGAACCGGGTTGACCGGTC
1 ACCGGTTTCAACCGGTTC-GAACCGGGTTGACCGGTC
1034333 TGACCCGACC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 2 0.06
38 23 0.70
39 8 0.24
ACGTcount: A:0.18, C:0.30, G:0.30, T:0.23
Consensus pattern (39 bp):
ACCGGTTTCAACCGGTTCGAACCGGGTTGACCGGTCCGA
Found at i:1034356 original size:12 final size:12
Alignment explanation
Indices: 1034339--1034388 Score: 68
Period size: 12 Copynumber: 4.3 Consensus size: 12
1034329 GGTCTGACCC
*
1034339 GACCCGACTGTT
1 GACCCGACCGTT
1034351 GACCCGACCGTT
1 GACCCGACCGTT
*
1034363 GACCCGACC--C
1 GACCCGACCGTT
1034373 GACCCGACCGTT
1 GACCCGACCGTT
1034385 GACC
1 GACC
1034389 GTTGACTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 9 0.27
12 24 0.73
ACGTcount: A:0.18, C:0.44, G:0.24, T:0.14
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:1038216 original size:9 final size:9
Alignment explanation
Indices: 1038202--1038285 Score: 78
Period size: 9 Copynumber: 8.8 Consensus size: 9
1038192 GGCTGCTGGA
1038202 AACCGGTTT
1 AACCGGTTT
1038211 AACCGGTTTTT
1 AACCGG--TTT
1038222 AACCGGTTT
1 AACCGGTTT
*
1038231 GACCGGTTT
1 AACCGGTTT
*
1038240 CAACCGGTTCG
1 -AACCGGTT-T
1038251 AACCGGTTT
1 AACCGGTTT
* *
1038260 GACCGGTCTG
1 AACCGGT-TT
1038270 AACCGGTTT
1 AACCGGTTT
*
1038279 GACCGGT
1 AACCGGT
1038286 CTGAATTGGG
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
9 30 0.49
10 22 0.36
11 9 0.15
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:1038227 original size:20 final size:20
Alignment explanation
Indices: 1038202--1038259 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
1038192 GGCTGCTGGA
*
1038202 AACCGGTTTAACCGGTTTTT
1 AACCGGTTTAACCGGTTTTC
*
1038222 AACCGGTTTGACCGG-TTTC
1 AACCGGTTTAACCGGTTTTC
*
1038241 AACCGGTTCGAACCGGTTT
1 AACCGGTT-TAACCGGTTT
1038260 GACCGGTCTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 11 0.34
20 19 0.59
21 2 0.06
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (20 bp):
AACCGGTTTAACCGGTTTTC
Found at i:1038246 original size:19 final size:19
Alignment explanation
Indices: 1038202--1038290 Score: 92
Period size: 19 Copynumber: 4.6 Consensus size: 19
1038192 GGCTGCTGGA
1038202 AACCGGTTT-AACCGGTTTTT
1 AACCGGTTTGAACCGG--TTT
1038222 AACCGGTTTG-ACCGGTTT
1 AACCGGTTTGAACCGGTTT
*
1038240 CAACCGGTTCGAACCGGTTT
1 -AACCGGTTTGAACCGGTTT
* *
1038260 GACCGGTCTGAACCGGTTT
1 AACCGGTTTGAACCGGTTT
* *
1038279 GACCGGTCTGAA
1 AACCGGTTTGAA
1038291 TTGGGTTGAC
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.05
19 37 0.60
20 22 0.35
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGAACCGGTTT
Found at i:1038254 original size:29 final size:28
Alignment explanation
Indices: 1038203--1038285 Score: 105
Period size: 29 Copynumber: 2.9 Consensus size: 28
1038193 GCTGCTGGAA
*
1038203 ACCGGTTTAACCGGTTTTTAACCGGTTTG
1 ACCGGTTTAACCGG-TTTGAACCGGTTTG
*
1038232 ACCGGTTTCAACCGGTTCGAACCGGTTTG
1 ACCGGTTT-AACCGGTTTGAACCGGTTTG
*
1038261 ACCGGTCTGAACCGGTTTG-ACCGGT
1 ACCGGT-TTAACCGGTTTGAACCGGT
1038286 CTGAATTGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 6 0.12
29 35 0.73
30 7 0.15
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (28 bp):
ACCGGTTTAACCGGTTTGAACCGGTTTG
Found at i:1038284 original size:38 final size:39
Alignment explanation
Indices: 1038223--1038308 Score: 97
Period size: 38 Copynumber: 2.3 Consensus size: 39
1038213 CCGGTTTTTA
* *
1038223 ACCGGTTTG-ACCGGTTTCAACCGGT-TCGAACCGGTTTG
1 ACCGGTCTGAACCGGTTTCAACCGGTCT-GAACCGGGTTG
* **
1038261 ACCGGTCTGAACCGGTTT-GACCGGTCTGAATTGGGTTG
1 ACCGGTCTGAACCGGTTTCAACCGGTCTGAACCGGGTTG
1038299 ACCGGTCTGA
1 ACCGGTCTGA
1038309 CCCGACCCGA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 32 0.78
39 9 0.22
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.28
Consensus pattern (39 bp):
ACCGGTCTGAACCGGTTTCAACCGGTCTGAACCGGGTTG
Found at i:1038299 original size:19 final size:19
Alignment explanation
Indices: 1038250--1038308 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
1038240 CAACCGGTTC
*
1038250 GAACCGGTTTGACCGGTCT
1 GAACCGGGTTGACCGGTCT
*
1038269 GAACCGGTTTGACCGGTCT
1 GAACCGGGTTGACCGGTCT
**
1038288 GAATTGGGTTGACCGGTCT
1 GAACCGGGTTGACCGGTCT
1038307 GA
1 GA
1038309 CCCGACCCGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.17, C:0.22, G:0.34, T:0.27
Consensus pattern (19 bp):
GAACCGGGTTGACCGGTCT
Found at i:1038317 original size:5 final size:5
Alignment explanation
Indices: 1038307--1038359 Score: 52
Period size: 5 Copynumber: 9.8 Consensus size: 5
1038297 TGACCGGTCT
* *
1038307 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
1038356 GACC
1 GACC
1038360 GTTGACCGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 32 0.80
7 8 0.20
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.08
Consensus pattern (5 bp):
GACCC
Found at i:1038328 original size:17 final size:17
Alignment explanation
Indices: 1038306--1038366 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 17
1038296 TTGACCGGTC
1038306 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1038323 TGACCCGACCCGACCCGACCGT
1 T-----GACCCGACCCGACCGT
1038345 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1038362 TGACC
1 TGACC
1038367 GTCGACTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
17 22 0.56
22 17 0.44
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:1038333 original size:22 final size:22
Alignment explanation
Indices: 1038307--1038359 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
1038297 TGACCGGTCT
1038307 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1038329 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
1038351 GACCCGACC
1 GACCCGACC
1038360 GTTGACCGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.51, G:0.23, T:0.08
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:1041701 original size:21 final size:21
Alignment explanation
Indices: 1041677--1041743 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1041667 TCATTCCTCG
1041677 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1041698 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1041719 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1041740 AGAG
1 AGAG
1041744 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1041701 original size:42 final size:42
Alignment explanation
Indices: 1041625--1041743 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1041615 GATTCGCCTG
* * *
1041625 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCTTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCTTA
* * * *
1041667 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCAC-TG
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC-CTTA
** * *
1041709 TCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 TCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1041744 CCCGATTCAC
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
42 57 0.92
43 5 0.08
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCTTA
Found at i:1043108 original size:14 final size:14
Alignment explanation
Indices: 1043089--1043124 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1043079 ATTGTTTAAT
1043089 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1043103 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1043117 TGATTTGT
1 TGATTTGT
1043125 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1043253 original size:19 final size:19
Alignment explanation
Indices: 1043242--1043280 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1043232 TCGCAATGCA
1043242 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGAG
1043261 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGAG
1043280 A
1 A
1043281 GAATCGCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.15, G:0.21, T:0.10
Consensus pattern (19 bp):
AAATGAAAATCGCAACGAG
Found at i:1043324 original size:19 final size:19
Alignment explanation
Indices: 1043302--1043452 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
1043292 CGAAATTAAA
1043302 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
1043321 TTCGCATTGCGA--TTCCC
1 TTCGCGTTGCGATTTTCAT
1043338 TT---GTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1043354 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1043368 TTCGTGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1043387 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1043402 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1043420 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1043439 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1043453 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 26 0.27
16 8 0.08
17 8 0.08
19 43 0.45
20 10 0.11
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1043349 original size:33 final size:32
Alignment explanation
Indices: 1043307--1043432 Score: 191
Period size: 33 Copynumber: 3.8 Consensus size: 32
1043297 TTAAATTCGC
1043307 GTTGCGATTTTCATTTCGCATTGCGATTCCCTT
1 GTTGCGATTTTCATTTCGCATTGCGATT-CCTT
*
1043340 GTTGCGATTTTCATTTCGCATTGCGAAATT-CGT
1 GTTGCGATTTTCATTTCGCATTGCG--ATTCCTT
*
1043373 GTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTC-CTT
1043406 GTTGCGATTTTCATTTCGCATTGCGAT
1 GTTGCGATTTTCATTTCGCATTGCGAT
1043433 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.44
Consensus pattern (32 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCCTT
Found at i:1043383 original size:66 final size:66
Alignment explanation
Indices: 1043299--1043431 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
1043289 ACGCGAAATT
*
1043299 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTTGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1043364 G
66 G
* *
1043365 AAATTCGTGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1043430 G
66 G
1043431 A
1 A
1043432 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.43
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1046808 original size:20 final size:20
Alignment explanation
Indices: 1046694--1046807 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
1046684 GATTCTGTAT
*
1046694 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1046714 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
1046734 TATCGTGTTGCGAAAGTTAG
1 TATCGCGTTGCGAAAGTCAG
** *
1046754 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
1046775 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1046795 TATCGCATTGCGA
1 TATCGCGTTGCGA
1046808 TTTTACCAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 60 0.76
21 14 0.18
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1046810 original size:41 final size:41
Alignment explanation
Indices: 1046674--1046811 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
1046664 AACTTTGAAA
* * *
1046674 ATCGCATTGCGATTCTGTATTATCTCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** * * *
1046715 ATCGCGTTGCGA--AAGTCAGTATCGTGTTGCGAAAGTTAGT
1 ATCGCATTGCGATTTTGT-ATTATCGCGTTGCGAAAGTCAGT
* *
1046755 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
1046796 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
1046812 ACCAATTCGC
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 30 0.38
41 45 0.57
42 2 0.03
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:1046822 original size:41 final size:41
Alignment explanation
Indices: 1046674--1046829 Score: 118
Period size: 41 Copynumber: 3.8 Consensus size: 41
1046664 AACTTTGAAA
* ** * * * *
1046674 ATCGCATTGCGATTCTGTATTATCTCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* *** * * * *
1046715 ATCGCGTTGCGAAAGT-CAGTATCGTGTTGCGAAAGTTAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* ** *
1046755 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
1046796 ATCGCATTGCGATTTTACCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
1046830 TTACTTATTC
Statistics
Matches: 91, Mismatches: 22, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
40 31 0.34
41 58 0.64
42 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
Found at i:1046839 original size:20 final size:21
Alignment explanation
Indices: 1046797--1046848 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1046787 ATAGTCAGTA
1046797 TCGCATTGCGATTTTACCAAT
1 TCGCATTGCGATTTTACCAAT
* **
1046818 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
1046838 TCGCATTGCGA
1 TCGCATTGCGA
1046849 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:1047530 original size:21 final size:21
Alignment explanation
Indices: 1047504--1047556 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1047494 GTTTCCAGAT
1047504 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
1047525 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
1047546 TCGCAATGCGA
1 TCGCAACGCGA
1047557 TTTTCCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:1047570 original size:21 final size:23
Alignment explanation
Indices: 1047552--1047955 Score: 312
Period size: 21 Copynumber: 18.9 Consensus size: 23
1047542 ACTATCGCAA
1047552 TGCGA-TT-TTCCAAATTCGCGT
1 TGCGATTTATTCCAAATTCGCGT
*
1047573 TGCGATTTATTCCAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGCGT
*
1047596 TGCGATTTATTCCAAATT--CTT
1 TGCGATTTATTCCAAATTCGCGT
1047617 TGCGATTTATTCCAAATTCGCGT
1 TGCGATTTATTCCAAATTCGCGT
* * * *
1047640 TGCGA--TAGTCGAAGTTCGCAT
1 TGCGATTTATTCCAAATTCGCGT
1047661 TGCGATTTATTCCAAATT--CGT
1 TGCGATTTATTCCAAATTCGCGT
1047682 TGCGATTTATTCCAAATTCGCGT
1 TGCGATTTATTCCAAATTCGCGT
* *
1047705 TACGA--TAGT-CAAAGTTCGCGT
1 TGCGATTTATTCCAAA-TTCGCGT
*
1047726 TGCGATTTATTCCAAGTT--CGT
1 TGCGATTTATTCCAAATTCGCGT
* * *
1047747 TGCGA--TAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGCGT
*
1047768 TGCGATTTATTCCAAGTT--CGT
1 TGCGATTTATTCCAAATTCGCGT
* * * *
1047789 TGC-A-ATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGCGT
*
1047810 TGCGATTTATTCCAAGTT--CGT
1 TGCGATTTATTCCAAATTCGCGT
* * *
1047831 TGCGA--TAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGCGT
*
1047852 TGCGATTTATTCCAAGTT--CGT
1 TGCGATTTATTCCAAATTCGCGT
* * *
1047873 TGCGA--TAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGCGT
*
1047894 TGCGATTTATTCCAAGTT--CGT
1 TGCGATTTATTCCAAATTCGCGT
* * *
1047915 TGCGA--TAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAATTCGCGT
*
1047936 TGCGATTTATTCCAAGTTCG
1 TGCGATTTATTCCAAATTCG
1047956 TTGCAATAGT
Statistics
Matches: 312, Mismatches: 39, Indels: 62
0.76 0.09 0.15
Matches are distributed among these distances:
19 45 0.14
20 5 0.02
21 152 0.49
22 3 0.01
23 104 0.33
24 3 0.01
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (23 bp):
TGCGATTTATTCCAAATTCGCGT
Found at i:1047766 original size:42 final size:42
Alignment explanation
Indices: 1047586--1047986 Score: 567
Period size: 42 Copynumber: 9.5 Consensus size: 42
1047576 GATTTATTCC
* * * *
1047586 AAGTTCGCGTTGCGATTTATTCCAAATTCTTTGCGATTTATTCC
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGA--TAGTCG
* * * * *
1047630 AAATTCGCGTTGCGA--TAGTCGAAGTTCGCATTGCGATTTATTCC
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCG--TTGCGA--TAGTCG
* * * *
1047674 AAATT--CGTTGCGATTTATTCCAAATTCGCGTTACGATAGTCA
1 AAGTTCGCGTTGCGATTTATTCCAAGTT--CGTTGCGATAGTCG
1047716 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
*
1047758 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCAATAGTCG
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
1047800 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
1047842 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
1047884 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
*
1047926 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCAATAGTCG
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
1047968 AAGTTCGCGTTGCGATTTA
1 AAGTTCGCGTTGCGATTTA
1047987 CTCATTGCGG
Statistics
Matches: 331, Mismatches: 18, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
42 263 0.79
44 66 0.20
46 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCG
Found at i:1048733 original size:21 final size:21
Alignment explanation
Indices: 1048707--1048812 Score: 85
Period size: 21 Copynumber: 5.0 Consensus size: 21
1048697 ATTTTGGACT
1048707 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
1048728 ATCGCAATGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
*
1048749 ATCGCAACGAATTTGTAATAA
1 ATCGCAACGAATTTGGAATAA
* *
1048770 ATCGCAACACGAACTTGGACT--
1 ATCGC-A-ACGAATTTGGAATAA
*
1048791 ATCGCAACAAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
1048812 A
1 A
1048813 AGTAACGCGA
Statistics
Matches: 64, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
19 18 0.28
20 1 0.02
21 25 0.39
22 1 0.02
23 19 0.30
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.24
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:1048752 original size:42 final size:42
Alignment explanation
Indices: 1048700--1048838 Score: 208
Period size: 42 Copynumber: 3.3 Consensus size: 42
1048690 CGTTGCGATT
*
1048700 TTGGACTATCGCAACGAATTTGGAATAAATCGCAATGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
1048742 TTCGACTATCGCAACGAATTTGTAATAAATCGCAACACGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
1048784 TTGGACTATCGCAACAAATTTGGAATAAA-AGTAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1048825 TTGGACTATCGCAA
1 TTGGACTATCGCAA
1048839 TGCGAATATG
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 23 0.26
42 64 0.74
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:1049418 original size:25 final size:26
Alignment explanation
Indices: 1049389--1049437 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
1049379 AAAATCTTAA
* *
1049389 TTTAAATATAAAT-TCCAATTTATGC
1 TTTAAACATAAATATCAAATTTATGC
1049414 TTTAAACATAAATATCAAATTTAT
1 TTTAAACATAAATATCAAATTTAT
1049438 TTTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (26 bp):
TTTAAACATAAATATCAAATTTATGC
Found at i:1049754 original size:11 final size:11
Alignment explanation
Indices: 1049738--1049764 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1049728 AAATCATTAA
1049738 ATTTATATTTT
1 ATTTATATTTT
1049749 ATTTATATTTT
1 ATTTATATTTT
1049760 ATTTA
1 ATTTA
1049765 AAATATTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTTATATTTT
Found at i:1050103 original size:5 final size:5
Alignment explanation
Indices: 1050089--1050127 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
1050079 ATATCTATAA
*
1050089 AAAAT TAAAT AAAAT AAAAT AAAAT AAAA- AATAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AAAA
1050128 AATAATCTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 2 0.07
5 26 0.87
6 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:1050128 original size:10 final size:10
Alignment explanation
Indices: 1050085--1050133 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
1050075 TTAAATATCT
1050085 ATAAAAAAT-
1 ATAAAAAATA
*
1050094 -TAAATAA-A
1 ATAAAAAATA
1050102 ATAAAATAA-A
1 ATAAAA-AATA
1050112 ATAAAAAATA
1 ATAAAAAATA
1050122 ATAAAAAATA
1 ATAAAAAATA
1050132 AT
1 AT
1050134 CTAGAATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
8 6 0.18
9 6 0.18
10 22 0.65
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
ATAAAAAATA
Found at i:1053255 original size:36 final size:36
Alignment explanation
Indices: 1053213--1053288 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
1053203 TTATAGCTAA
*
1053213 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1053249 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1053285 AAAA
1 AAAA
1053289 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:1055831 original size:44 final size:44
Alignment explanation
Indices: 1055777--1055873 Score: 167
Period size: 44 Copynumber: 2.2 Consensus size: 44
1055767 TTATTCTATA
1055777 TTTTAGTTAATTTTTTATTAAATAATGTAGTTCAAAATGCGTAG
1 TTTTAGTTAATTTTTTATTAAATAATGTAGTTCAAAATGCGTAG
* * *
1055821 TTTTAGTTAATTTTTTATTAGATTATGTAGTTCAAAATGTGTAG
1 TTTTAGTTAATTTTTTATTAAATAATGTAGTTCAAAATGCGTAG
1055865 TTTTAGTTA
1 TTTTAGTTA
1055874 TACCATTAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.31, C:0.03, G:0.14, T:0.52
Consensus pattern (44 bp):
TTTTAGTTAATTTTTTATTAAATAATGTAGTTCAAAATGCGTAG
Found at i:1056109 original size:7 final size:7
Alignment explanation
Indices: 1056097--1056137 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
1056087 CACTAAATTT
1056097 AATTTAA
1 AATTTAA
1056104 AATTTAA
1 AATTTAA
1056111 AATTTAA
1 AATTTAA
*
1056118 AATATAA
1 AATTTAA
1056125 AATCTT-A
1 AAT-TTAA
1056132 AATTTA
1 AATTTA
1056138 TTTTTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 2 0.07
7 27 0.90
8 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (7 bp):
AATTTAA
Found at i:1059767 original size:22 final size:21
Alignment explanation
Indices: 1059742--1059782 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1059732 AGCTCGTATC
1059742 ATTGCACCGAAGTGCACATAGA
1 ATTGCACCGAAGTGC-CATAGA
*
1059764 ATTGCACCGTAGTGCCATA
1 ATTGCACCGAAGTGCCATA
1059783 TAATAATGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (21 bp):
ATTGCACCGAAGTGCCATAGA
Found at i:1059821 original size:21 final size:21
Alignment explanation
Indices: 1059795--1059882 Score: 167
Period size: 21 Copynumber: 4.2 Consensus size: 21
1059785 ATAATGTCTA
1059795 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
*
1059816 TAAGGACTACATATCATTCCT
1 TAAGGACCACATATCATTCCT
1059837 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
1059858 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
1059879 TAAG
1 TAAG
1059883 AATCATATAC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (21 bp):
TAAGGACCACATATCATTCCT
Found at i:1068145 original size:30 final size:31
Alignment explanation
Indices: 1068111--1068198 Score: 108
Period size: 30 Copynumber: 2.8 Consensus size: 31
1068101 GAAAAAGAAT
*
1068111 ATGTGATATGTGAAAGTGAATCATATGA-AA
1 ATGTGATATGTGAAAGTGAACCATATGATAA
* *
1068141 ATGTGCTACGT-ACAAGTGAACCATATGATTAA
1 ATGTGATATGTGA-AAGTGAACCATATGA-TAA
*
1068173 ATTTGATATGTGAAAGTGAACCATAT
1 ATGTGATATGTGAAAGTGAACCATAT
1068199 ATATATATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
29 1 0.02
30 23 0.48
32 23 0.48
33 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (31 bp):
ATGTGATATGTGAAAGTGAACCATATGATAA
Found at i:1068466 original size:32 final size:32
Alignment explanation
Indices: 1068393--1068528 Score: 120
Period size: 31 Copynumber: 4.3 Consensus size: 32
1068383 GTTCTACAGA
* * *
1068393 ACATATAGACAGAATTACCTATTTCTTTCGGG
1 ACATATGGACAAAATTACCTATGTCTTTCGGG
*
1068425 -CATATGGACAAAATTACCTATGTCTTTTGGG
1 ACATATGGACAAAATTACCTATGTCTTTCGGG
* ** *
1068456 ACATATGGACAATA-TACCTATGT-TCTAAGGA
1 ACATATGGACAAAATTACCTATGTCT-TTCGGG
* *
1068487 ACATATGGAC-AATTTACCTAGGT-TCTTCGGG
1 ACATATGGACAAAATTACCTATGTCT-TTCGGG
*
1068518 ACCTATGGACA
1 ACATATGGACA
1068529 GTTGTCGAGG
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
30 2 0.02
31 71 0.84
32 12 0.14
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (32 bp):
ACATATGGACAAAATTACCTATGTCTTTCGGG
Found at i:1069214 original size:19 final size:19
Alignment explanation
Indices: 1069188--1069237 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
1069178 TATTGTTTAT
1069188 TACTGTTCATA-CAGTATAG
1 TACTGTTCATAGC-GTATAG
*
1069207 TGCTGTTCATAGCGTATAG
1 TACTGTTCATAGCGTATAG
1069226 TACTGTTCATAG
1 TACTGTTCATAG
1069238 ATACATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 27 0.96
20 1 0.04
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (19 bp):
TACTGTTCATAGCGTATAG
Found at i:1070096 original size:22 final size:23
Alignment explanation
Indices: 1070071--1070115 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1070061 TGTAGCAGGG
*
1070071 TACTGTTC-ACGGTATTGTTCAA
1 TACTGTTCAACGGTACTGTTCAA
1070093 TACTGTTCATACGGTACTGTTCA
1 TACTGTTCA-ACGGTACTGTTCA
1070116 CTGTTCATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
24 12 0.60
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (23 bp):
TACTGTTCAACGGTACTGTTCAA
Found at i:1070638 original size:21 final size:20
Alignment explanation
Indices: 1070612--1070669 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 20
1070602 ATCCTCTAGC
*
1070612 AAAAGGATTGATCCCTTTGA
1 AAAAGGATCGATCCCTTTGA
* *
1070632 CCAAAGGATCGATCCCCTTGA
1 -AAAAGGATCGATCCCTTTGA
1070653 AAAAGGATCGATCCCTT
1 AAAAGGATCGATCCCTT
1070670 GGATAACATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
AAAAGGATCGATCCCTTTGA
Found at i:1070657 original size:41 final size:41
Alignment explanation
Indices: 1070592--1070669 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1070582 ATTTTTTGCT
* * *
1070592 CAAACGATCGATCCTCTAGCAAAAGGATTGATCCCTTTGAC
1 CAAACGATCGATCCCCTAGAAAAAGGATCGATCCCTTTGAC
* *
1070633 CAAAGGATCGATCCCCTTGAAAAAGGATCGATCCCTT
1 CAAACGATCGATCCCCTAGAAAAAGGATCGATCCCTT
1070670 GGATAACATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (41 bp):
CAAACGATCGATCCCCTAGAAAAAGGATCGATCCCTTTGAC
Found at i:1070659 original size:20 final size:20
Alignment explanation
Indices: 1070597--1070667 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
1070587 TTGCTCAAAC
* * *
1070597 GATCGATCCTCTAGCAAAAG
1 GATCGATCCCCTTGAAAAAG
* * *
1070617 GATTGATCCCTTTGACCAAAG
1 GATCGATCCCCTTGA-AAAAG
1070638 GATCGATCCCCTTGAAAAAG
1 GATCGATCCCCTTGAAAAAG
1070658 GATCGATCCC
1 GATCGATCCC
1070668 TTGGATAACA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 24 0.59
21 17 0.41
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (20 bp):
GATCGATCCCCTTGAAAAAG
Found at i:1071295 original size:14 final size:14
Alignment explanation
Indices: 1071276--1071304 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1071266 AAACTATTTT
1071276 ATATTATTTTTTAA
1 ATATTATTTTTTAA
1071290 ATATTATTTTTTAA
1 ATATTATTTTTTAA
1071304 A
1 A
1071305 AAAGAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATATTATTTTTTAA
Found at i:1071927 original size:2 final size:2
Alignment explanation
Indices: 1071920--1071965 Score: 74
Period size: 2 Copynumber: 22.0 Consensus size: 2
1071910 AAATTTAATA
1071920 AT AT AT AT AT AT AT AT AT AT AT GAT AT AT AT AT AT AT AT AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT -AT
1071964 AT
1 AT
1071966 TATTATTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 38 0.90
3 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1071948 original size:19 final size:19
Alignment explanation
Indices: 1071920--1071965 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1071910 AAATTTAATA
1071920 ATAT-ATATATATATATAT
1 ATATGATATATATATATAT
1071938 ATATGATATATATATATAT
1 ATATGATATATATATATAT
1071957 ATATGATAT
1 ATATGATAT
1071966 TATTATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (19 bp):
ATATGATATATATATATAT
Found at i:1073177 original size:2 final size:2
Alignment explanation
Indices: 1073170--1073195 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1073160 ATGTAAATCG
1073170 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1073196 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1074715 original size:2 final size:2
Alignment explanation
Indices: 1074708--1074746 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1074698 CTGTAATCAT
1074708 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1074747 TCTGTTTTGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1077181 original size:2 final size:2
Alignment explanation
Indices: 1077174--1077233 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
1077164 GTCCATATTT
*
1077174 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1077216 TA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1077234 GTTTACAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1077339 original size:36 final size:36
Alignment explanation
Indices: 1077222--1077513 Score: 200
Period size: 36 Copynumber: 8.2 Consensus size: 36
1077212 TATATATATG
** **
1077222 TATAT-ATATATAGTTTACAAATGATTTTTG-AAA-
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
* *
1077255 -ATATGATATATAGTTTTTAAAACATTTTTTGAAACT
1 TATATAATATATAGTTTTTAAAACA-TTTTTGAAAAT
* *
1077291 ATATATATTATATAGTTTTTAAAACATTTTCGAAAAT
1 -TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
* *
1077328 TATATAATATATAGTTTTTAAAATATTTTTAAAAAAT
1 TATATAATATATAGTTTTTAAAACATTTTT-GAAAAT
* **
1077365 TATAT-AT-TATA-TTTTT--GA-ATTTTTTTAAA-
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
*
1077394 TATATAATATATAGTTTTTTAAATCA-TTTTGAAAACT
1 TATATAATATATAG-TTTTTAAAACATTTTTGAAAA-T
* *
1077431 TATATAATATAT--TTTTGGAAAAAATATTTATGAAAACAAT
1 TATATAATATATAGTTTT-TAAAACAT-TTT-TG--AA-AAT
* * *
1077471 TATATATTATATAGTTTTCAAAAACATGTTTGAAAA-
1 TATATAATATATAGTTTT-TAAAACATTTTTGAAAAT
1077507 TATATAA
1 TATATAA
1077514 ATTTAAAATA
Statistics
Matches: 205, Mismatches: 29, Indels: 47
0.73 0.10 0.17
Matches are distributed among these distances:
29 5 0.02
30 5 0.02
31 10 0.05
32 5 0.02
33 20 0.10
34 15 0.07
35 17 0.08
36 36 0.18
37 36 0.18
38 26 0.13
40 16 0.08
41 4 0.02
42 10 0.05
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.47
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTTGAAAAT
Found at i:1077601 original size:2 final size:2
Alignment explanation
Indices: 1077594--1077627 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1077584 ATAATTTTAA
1077594 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1077628 TATTTCTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1078925 original size:12 final size:13
Alignment explanation
Indices: 1078908--1078939 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1078898 TCAAATCGAA
1078908 TAATTTTAA-TTT
1 TAATTTTAATTTT
1078920 TAATTTTAATTTT
1 TAATTTTAATTTT
1078933 TAATTTT
1 TAATTTT
1078940 TGCAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TAATTTTAATTTT
Found at i:1078940 original size:7 final size:6
Alignment explanation
Indices: 1078908--1078939 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
1078898 TCAAATCGAA
1078908 TAATTT TAATTT TAATTT TAATTTT TAATTT T
1 TAATTT TAATTT TAATTT TAA-TTT TAATTT T
1078940 TGCAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TAATTT
Found at i:1079500 original size:18 final size:20
Alignment explanation
Indices: 1079479--1079516 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1079469 TTGATTCTTT
1079479 TAATATT-AAT-TTTTTTTA
1 TAATATTAAATATTTTTTTA
1079497 TAATATTAAATATTTTTTTA
1 TAATATTAAATATTTTTTTA
1079517 AAATTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 3 0.17
20 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TAATATTAAATATTTTTTTA
Found at i:1080140 original size:20 final size:20
Alignment explanation
Indices: 1080115--1080152 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1080105 TTTGGTTTAC
1080115 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
1080135 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
1080153 GGAATATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:1080376 original size:33 final size:34
Alignment explanation
Indices: 1080313--1080377 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
1080303 AAAATATTTA
*
1080313 TATATTTTCTTTAAAAAATTAAATTCATAAAATT
1 TATATTTTCTTTAAAAAATTAAAATCATAAAATT
*
1080347 TATATTTT-TTTACAAAATTGAAAAT-ATAAAA
1 TATATTTTCTTTAAAAAATT-AAAATCATAAAA
1080378 AGGTTTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.45
Consensus pattern (34 bp):
TATATTTTCTTTAAAAAATTAAAATCATAAAATT
Found at i:1082497 original size:13 final size:13
Alignment explanation
Indices: 1082453--1082499 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1082443 ATGTTCTTTG
*
1082453 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
1082467 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
1082479 TTTATTTAAAATAA
1 -ATATTTAAAATAA
1082493 ATATTTA
1 ATATTTA
1082500 TTTATATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:1083941 original size:3 final size:3
Alignment explanation
Indices: 1083933--1084026 Score: 170
Period size: 3 Copynumber: 31.3 Consensus size: 3
1083923 TTAATATATT
*
1083933 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
1083981 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1084027 GATATGGGTA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 87 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1084689 original size:113 final size:113
Alignment explanation
Indices: 1084347--1085020 Score: 963
Period size: 113 Copynumber: 5.9 Consensus size: 113
1084337 GATAGAATTA
* * *
1084347 TTGAACAAGTTCTTCTTATTATAAACTTCTTATTCCTTCTTCAGATGATGAGTTCTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTAT
* *
1084412 GAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAG
63 GAACTCTTCCTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAG
*
1084463 TTGAACAAGTTCCTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
* *
1084528 GAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAG
63 GAACTCTTCCTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAG
1084579 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
1084644 CTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAG
66 CTCTTCCTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAG
1084692 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
** * * * * * *
1084757 CT-TTCTCTGGAAAAAATAATACATCCAGTGATGAATTCAGACAAAAGG
66 CTCTTC-CTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAG
*
1084805 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * ** * * * * *
1084870 CTTTTTTCTGGAAAAAATAATCCATCCAGTGATGAATTCAGACAAAAGG
66 C-TCTTCCTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAG
*
1084919 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
1084984 GAACTCTTCCTCTGGAAATGATGATCCATCAAATGAT
63 GAACTCTT-C-CTGGAAATGATGATCCATCAAATGAT
1085021 AGATTTGAAT
Statistics
Matches: 522, Mismatches: 25, Indels: 20
0.92 0.04 0.04
Matches are distributed among these distances:
112 3 0.01
113 234 0.45
114 89 0.17
115 2 0.00
116 153 0.29
117 20 0.04
118 21 0.04
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (113 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTCTTCCTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAG
Found at i:1085859 original size:83 final size:83
Alignment explanation
Indices: 1085759--1086224 Score: 898
Period size: 83 Copynumber: 5.6 Consensus size: 83
1085749 TCCTACCACT
1085759 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
*
1085824 GATTGGTTCTG-CCACACC
66 GATTGATTCTGTCCA-ACC
1085842 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
1085907 GATTGATTCTGTCCAACC
66 GATTGATTCTGTCCAACC
1085925 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
1085990 GATTGATTCTGTCCAACC
66 GATTGATTCTGTCCAACC
*
1086008 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTAAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
1086073 GATTGATTCTGTCCAACC
66 GATTGATTCTGTCCAACC
1086091 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
1086156 GATTGATTCTGTCCAACC
66 GATTGATTCTGTCCAACC
1086174 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
1086225 AATTCTGCCA
Statistics
Matches: 379, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
83 376 0.99
84 3 0.01
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (83 bp):
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAAT
GATTGATTCTGTCCAACC
Found at i:1087270 original size:9 final size:9
Alignment explanation
Indices: 1087256--1087314 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
1087246 TTGACCCCCC
1087256 TTTTTCTTT
1 TTTTTCTTT
1087265 TTTTTCTTT
1 TTTTTCTTT
1087274 TTTTT-TTGT
1 TTTTTCTT-T
*
1087283 TCTTTTTTTT
1 T-TTTTCTTT
1087293 TTTTTACTTT
1 TTTTT-CTTT
*
1087303 TTTTACTTT
1 TTTTTCTTT
1087312 TTT
1 TTT
1087315 CTTCAAGCAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
8 2 0.05
9 27 0.61
10 13 0.30
11 2 0.05
ACGTcount: A:0.03, C:0.08, G:0.02, T:0.86
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:1087286 original size:23 final size:22
Alignment explanation
Indices: 1087256--1087314 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 22
1087246 TTGACCCCCC
1087256 TTTTTCTTTTTTTTCTTTTT-TT
1 TTTTTCTTTTTTTT-TTTTTATT
1087278 TTTGTTCTTTTTTTTTTTTTACTT
1 TTT-TTCTTTTTTTTTTTTTA-TT
1087302 TTTTTACTTTTTT
1 TTTTT-CTTTTTT
1087315 CTTCAAGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.24
23 13 0.39
24 12 0.36
ACGTcount: A:0.03, C:0.08, G:0.02, T:0.86
Consensus pattern (22 bp):
TTTTTCTTTTTTTTTTTTTATT
Found at i:1097874 original size:32 final size:30
Alignment explanation
Indices: 1097838--1097918 Score: 74
Period size: 32 Copynumber: 2.6 Consensus size: 30
1097828 CAAATAATGA
*
1097838 AATAAA-ATACTTGAAAAATAAAATGAAACATT
1 AATAAATATACAT-AAAAATAAAATGAAA-A-T
* *
1097870 AATAAATATACATATAAATAATATGAAAAT
1 AATAAATATACATAAAAATAAAATGAAAAT
* * *
1097900 AATAAGTATATATACAAAT
1 AATAAATATACATAAAAAT
1097919 TTTGAAAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
30 17 0.40
31 1 0.02
32 19 0.45
33 5 0.12
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (30 bp):
AATAAATATACATAAAAATAAAATGAAAAT
Found at i:1098610 original size:13 final size:13
Alignment explanation
Indices: 1098566--1098612 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1098556 ATGTTCTTTG
*
1098566 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
1098580 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
1098592 TTTATTTAAAATAA
1 -ATATTTAAAATAA
1098606 ATATTTA
1 ATATTTA
1098613 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:1100056 original size:3 final size:3
Alignment explanation
Indices: 1100048--1100128 Score: 137
Period size: 3 Copynumber: 27.3 Consensus size: 3
1100038 TTAATATATT
* *
1100048 TAA TAA TAA TAA TAA T-A TAA TTA TAA TAA TAA TAA TAA TAA GAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1100095 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1100129 GATATGGGTA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
2 2 0.03
3 71 0.97
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1104500 original size:2 final size:2
Alignment explanation
Indices: 1104493--1104537 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1104483 AATGTTTTTA
1104493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1104535 AT A
1 AT A
1104538 GATAAAGAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1105124 original size:15 final size:15
Alignment explanation
Indices: 1105084--1105125 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
1105074 AAAAAATAAC
*
1105084 ATTTTAATATATTTAT
1 ATTTTAAT-TTTTTAT
1105100 A-TTTATATTTTTTAT
1 ATTTTA-ATTTTTTAT
1105115 ATTTTAATTTT
1 ATTTTAATTTT
1105126 ATAATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTAATTTTTTAT
Found at i:1106647 original size:21 final size:22
Alignment explanation
Indices: 1106600--1106648 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
1106590 TTGGGGTAAG
*
1106600 TGGGTGGCTTAGTCGGAGGAGT
1 TGGGTGGCTTAGTCGGAGGACT
* *
1106622 T-GGTGGCTTGGTCGGTGG-CT
1 TGGGTGGCTTAGTCGGAGGACT
1106642 TGGGTGG
1 TGGGTGG
1106649 AGGATAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 20 0.87
22 1 0.04
ACGTcount: A:0.06, C:0.10, G:0.53, T:0.31
Consensus pattern (22 bp):
TGGGTGGCTTAGTCGGAGGACT
Found at i:1106719 original size:39 final size:38
Alignment explanation
Indices: 1106676--1106949 Score: 148
Period size: 39 Copynumber: 7.1 Consensus size: 38
1106666 TGGTTGGCGC
*
1106676 CTTGGGTGGTGCTTTTGGAGGAGGACCATAAGTTGGAGG
1 CTTGGGTGGTGCTTTTGGAGGAGGA-CATAAGTTGGTGG
* * * * * **
1106715 CTTGGTTGGTGCCTTGGGTGGAGG--GTAAACTGGTGG
1 CTTGGGTGGTGCTTTTGGAGGAGGACATAAGTTGGTGG
* * *
1106751 CTTAGGTGGTGTTTTTGGCGGAGGAGCATAAGTTGGTGG
1 CTTGGGTGGTGCTTTTGGAGGAGGA-CATAAGTTGGTGG
* * * *** *
1106790 CTTGGTTGGTGTCTTGGGTGGA-GAGG--GTAAACCGGTGA
1 CTTGGGTGGTG-CTT--TTGGAGGAGGACATAAGTTGGTGG
** * *
1106828 CTTGGGTGGTATTTTTGGCGGAGGAGCATGAGTTGGTGG
1 CTTGGGTGGTGCTTTTGGAGGAGGA-CATAAGTTGGTGG
* * * * **
1106867 CTTGGTTGGTG-TCTTGGGTGGAGGAGAGT-AGACCGGTGG
1 CTTGGGTGGTGCT-TTTGGAGGAGGACA-TAAG-TTGGTGG
*
1106906 CTTGGGTGGTGCTTTTGGAGGAGGAGCATAGGTTGGTGG
1 CTTGGGTGGTGCTTTTGGAGGAGGA-CATAAGTTGGTGG
1106945 CTTGG
1 CTTGG
1106950 TTGGAGCCTT
Statistics
Matches: 167, Mismatches: 52, Indels: 32
0.67 0.21 0.13
Matches are distributed among these distances:
35 3 0.02
36 30 0.18
37 2 0.01
38 20 0.12
39 100 0.60
40 5 0.03
41 4 0.02
42 3 0.02
ACGTcount: A:0.14, C:0.09, G:0.46, T:0.31
Consensus pattern (38 bp):
CTTGGGTGGTGCTTTTGGAGGAGGACATAAGTTGGTGG
Found at i:1106933 original size:78 final size:76
Alignment explanation
Indices: 1106676--1106965 Score: 402
Period size: 77 Copynumber: 3.8 Consensus size: 76
1106666 TGGTTGGCGC
* *
1106676 CTTGGGTGGTGCTTTTGGAGGAGGACCATAAGTTGGAGGCTTGGTTGGTGCCTTGGGTGGAG-GG
1 CTTGGGTGGTGCTTTTGGAGGAGGAGCATAAGTTGGTGGCTTGGTTGGTGCCTTGGGTGGAGAGG
*
1106740 TAAACTGGTGG
66 TAAACCGGTGG
* * * *
1106751 CTTAGGTGGTGTTTTTGGCGGAGGAGCATAAGTTGGTGGCTTGGTTGGTGTCTTGGGTGGAGAGG
1 CTTGGGTGGTGCTTTTGGAGGAGGAGCATAAGTTGGTGGCTTGGTTGGTGCCTTGGGTGGAGA-G
*
1106816 GTAAACCGGTGA
65 GTAAACCGGTGG
** * * *
1106828 CTTGGGTGGTATTTTTGGCGGAGGAGCATGAGTTGGTGGCTTGGTTGGTGTCTTGGGTGGAGGAG
1 CTTGGGTGGTGCTTTTGGAGGAGGAGCATAAGTTGGTGGCTTGGTTGGTGCCTTGGGTGGA-GAG
*
1106893 AGTAGACCGGTGG
65 -GTAAACCGGTGG
* *
1106906 CTTGGGTGGTGCTTTTGGAGGAGGAGCATAGGTTGGTGGCTTGGTTGGAGCCTTGGGTGG
1 CTTGGGTGGTGCTTTTGGAGGAGGAGCATAAGTTGGTGGCTTGGTTGGTGCCTTGGGTGG
1106966 TGGTGGATAA
Statistics
Matches: 191, Mismatches: 20, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
75 56 0.29
77 70 0.37
78 65 0.34
ACGTcount: A:0.13, C:0.10, G:0.46, T:0.31
Consensus pattern (76 bp):
CTTGGGTGGTGCTTTTGGAGGAGGAGCATAAGTTGGTGGCTTGGTTGGTGCCTTGGGTGGAGAGG
TAAACCGGTGG
Found at i:1106961 original size:155 final size:152
Alignment explanation
Indices: 1106676--1106965 Score: 418
Period size: 155 Copynumber: 1.9 Consensus size: 152
1106666 TGGTTGGCGC
*
1106676 CTTGGGTGGTGCTTTTGGAGGAGGACCATAAGTTGGAGGCTTGGTTGGTGCCTTGGGTGGAGGGT
1 CTTGGGTGGTACTTTTGGAGGAGGACCATAAGTTGGAGGCTTGGTTGGTGCCTTGGGTGGAGGGT
* * * * *
1106741 AAACTGGTGGCTTAGGTGGTGTTTTTGGCGGAGGAGCATAAGTTGGTGGCTTGGTTGGTGTCTTG
66 AAACCGGTGGCTTAGGTGGTGCTTTTGGAGGAGGAGCATAAGTTGGTGGCTTGGTTGGAGCCTTG
1106806 GGTGGAGAGGGTAAACCGGTGA
131 GGTGGAGAGGGTAAACCGGTGA
* * * * * *
1106828 CTTGGGTGGTATTTTTGGCGGAGGAGCATGAGTTGGTGGCTTGGTTGGTGTCTTGGGTGGAGGAG
1 CTTGGGTGGTACTTTTGGAGGAGGACCATAAGTTGGAGGCTTGGTTGGTGCCTTGGGTGGA-G-G
* * *
1106893 AGTAGACCGGTGGCTTGGGTGGTGCTTTTGGAGGAGGAGCATAGGTTGGTGGCTTGGTTGGAGCC
64 -GTAAACCGGTGGCTTAGGTGGTGCTTTTGGAGGAGGAGCATAAGTTGGTGGCTTGGTTGGAGCC
1106958 TTGGGTGG
128 TTGGGTGG
1106966 TGGTGGATAA
Statistics
Matches: 120, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
152 54 0.45
153 1 0.01
154 1 0.01
155 64 0.53
ACGTcount: A:0.13, C:0.10, G:0.46, T:0.31
Consensus pattern (152 bp):
CTTGGGTGGTACTTTTGGAGGAGGACCATAAGTTGGAGGCTTGGTTGGTGCCTTGGGTGGAGGGT
AAACCGGTGGCTTAGGTGGTGCTTTTGGAGGAGGAGCATAAGTTGGTGGCTTGGTTGGAGCCTTG
GGTGGAGAGGGTAAACCGGTGA
Found at i:1106983 original size:78 final size:76
Alignment explanation
Indices: 1106676--1106983 Score: 402
Period size: 78 Copynumber: 4.0 Consensus size: 76
1106666 TGGTTGGCGC
* *
1106676 CTTGGGTGGTGCTTTTGGAGGAGGACCATAAGTTGGAGGCTTGGTTGGTGCCTTGGGTGGA-GGG
1 CTTGGGTGGTGCTTTTGGAGGAGGAGCATAAGTTGGTGGCTTGGTTGGTGCCTTGGGTGGAGGGG
*
1106740 TAAACTGGTGG
66 TAAACCGGTGG
* * * *
1106751 CTTAGGTGGTGTTTTTGGCGGAGGAGCATAAGTTGGTGGCTTGGTTGGTGTCTTGGGTGGAGAGG
1 CTTGGGTGGTGCTTTTGGAGGAGGAGCATAAGTTGGTGGCTTGGTTGGTGCCTTGGGTGGAG-GG
*
1106816 GTAAACCGGTGA
65 GTAAACCGGTGG
** * * *
1106828 CTTGGGTGGTATTTTTGGCGGAGGAGCATGAGTTGGTGGCTTGGTTGGTGTCTTGGGTGGAGGAG
1 CTTGGGTGGTGCTTTTGGAGGAGGAGCATAAGTTGGTGGCTTGGTTGGTGCCTTGGGTGGAGG-G
*
1106893 AGTAGACCGGTGG
65 -GTAAACCGGTGG
* * *
1106906 CTTGGGTGGTGCTTTTGGAGGAGGAGCATAGGTTGGTGGCTTGGTTGGAGCCTTGGGTGGTGGTG
1 CTTGGGTGGTGCTTTTGGAGGAGGAGCATAAGTTGGTGGCTTGGTTGGTGCCTTGGGTGGAGG-G
*
1106971 GATAAACAGGTGG
65 G-TAAACCGGTGG
1106984 AGCCGTCGGG
Statistics
Matches: 204, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
75 55 0.27
76 1 0.00
77 73 0.36
78 75 0.37
ACGTcount: A:0.14, C:0.09, G:0.46, T:0.30
Consensus pattern (76 bp):
CTTGGGTGGTGCTTTTGGAGGAGGAGCATAAGTTGGTGGCTTGGTTGGTGCCTTGGGTGGAGGGG
TAAACCGGTGG
Found at i:1107481 original size:16 final size:18
Alignment explanation
Indices: 1107446--1107488 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1107436 AATTGATATA
*
1107446 ATTATATATATTATTTTT
1 ATTATTTATATTATTTTT
1107464 ATTATTTATA-TA-TTTT
1 ATTATTTATATTATTTTT
1107480 ATTAATTTA
1 ATT-ATTTA
1107489 ATTTTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 7 0.30
18 9 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTATTTATATTATTTTT
Found at i:1107918 original size:41 final size:41
Alignment explanation
Indices: 1107849--1107944 Score: 149
Period size: 41 Copynumber: 2.3 Consensus size: 41
1107839 GTGCGGACCC
* *
1107849 GGGGGCGCGCCTTAGGCCACCAAGGAGTATAGCGCAGGGCA
1 GGGGTCGCGCCTTAGGCCACCAAGGAGTATAGCGCAAGGCA
*
1107890 GGTGTCGCGCCTTAGGCCACCTAA-GAGTATAGCGCAAGGCA
1 GGGGTCGCGCCTTAGGCCACC-AAGGAGTATAGCGCAAGGCA
1107931 GGGGTCGCGCCTTA
1 GGGGTCGCGCCTTA
1107945 CCTTTAACAC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 48 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.27, G:0.38, T:0.15
Consensus pattern (41 bp):
GGGGTCGCGCCTTAGGCCACCAAGGAGTATAGCGCAAGGCA
Found at i:1108019 original size:15 final size:15
Alignment explanation
Indices: 1107999--1108029 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1107989 CTTTATCTGA
1107999 TATAATTATGTAAGG
1 TATAATTATGTAAGG
1108014 TATAATTATGTAAGG
1 TATAATTATGTAAGG
1108029 T
1 T
1108030 GCGGTGCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (15 bp):
TATAATTATGTAAGG
Found at i:1112061 original size:32 final size:32
Alignment explanation
Indices: 1112020--1112085 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
1112010 CCTCCATGAG
*** *
1112020 GGGTCATAAAACTTTGTGAAGGTGGCGGCGGC
1 GGGTCATAAAACCAGGTAAAGGTGGCGGCGGC
1112052 GGGTCATAAAACCAGGTAAAGGTGGCGGCGGC
1 GGGTCATAAAACCAGGTAAAGGTGGCGGCGGC
1112084 GG
1 GG
1112086 TATCTGGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.24, C:0.17, G:0.42, T:0.17
Consensus pattern (32 bp):
GGGTCATAAAACCAGGTAAAGGTGGCGGCGGC
Found at i:1113446 original size:206 final size:209
Alignment explanation
Indices: 1113093--1113508 Score: 722
Period size: 206 Copynumber: 2.0 Consensus size: 209
1113083 GAGCCCCAAC
1113093 TGAGTGATCCGCCAGACGAAAGTCGACAAGATATCGCAACCACATACAAGAACTTGGTTGCGCGA
1 TGAGTGATCCGCCAGACGAAAGTCGACAAGATATCGCAACCACATACAAGAACTTGGTTGCGCGA
1113158 TTTGTCCGGCATCAACAACCCTCATCAGCTGCAGTATGCATGCCGTGCATACATTTAATTTCATC
66 TTTGTCCGGCATCAACAACCCTCATCAGCTGCAGTATGCATGCCGTGCATACATTTAATTT-ATC
1113223 ATCTGACGCGTCCTCGTTCAACT-CCGAAAATTGGCATCTAA-C-ATTTAACGGTAT-CGACCA-
130 ATCTGACGCGTCCTCGTTCAACTCCCGAAAATTGGCATCTAACCAATTTAACGGTATCCGACCAC
1113283 CGTTAAAACTTTCTG
195 CGTTAAAACTTTCTG
1113298 TGAGTGATCCGGCCAGACG-AAGTCGACAAGATATCGCAACCACATACAATGAACTTGGTTGCGC
1 TGAGTGATCC-GCCAGACGAAAGTCGACAAGATATCGCAACCACATACAA-GAACTTGGTTGCGC
1113362 GATTTGTCCGGCATCAACAACCCTCCTATCAGCTGCAGTATGCATGCCGTGCATACATTTTAA-T
64 GATTTGTCCGGCATCAACAACCCT-C-ATCAGCTGCAGTATGCATGCCGTGCATACA-TTTAATT
1113426 T-TCATCTGACGCGTCCTCGTTCAACTCCCGAAAATTGGCATCTAACCAATTTAACGGTATCCGA
126 TATCATCTGACGCGTCCTCGTTCAACTCCCGAAAATTGGCATCTAACCAATTTAACGGTATCCGA
1113490 CCACCGTTAAAACTTTCTG
191 CCACCGTTAAAACTTTCTG
1113509 GGACACGTCC
Statistics
Matches: 201, Mismatches: 0, Indels: 14
0.93 0.00 0.07
Matches are distributed among these distances:
205 40 0.20
206 71 0.35
207 19 0.09
208 33 0.16
209 17 0.08
210 6 0.03
211 15 0.07
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (209 bp):
TGAGTGATCCGCCAGACGAAAGTCGACAAGATATCGCAACCACATACAAGAACTTGGTTGCGCGA
TTTGTCCGGCATCAACAACCCTCATCAGCTGCAGTATGCATGCCGTGCATACATTTAATTTATCA
TCTGACGCGTCCTCGTTCAACTCCCGAAAATTGGCATCTAACCAATTTAACGGTATCCGACCACC
GTTAAAACTTTCTG
Found at i:1114017 original size:17 final size:17
Alignment explanation
Indices: 1113995--1114028 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1113985 AAAAAATTAA
1113995 TTAAATAAAATAAATAC
1 TTAAATAAAATAAATAC
*
1114012 TTAAATAAATTAAATAC
1 TTAAATAAAATAAATAC
1114029 AAAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAAATAAAATAAATAC
Found at i:1118363 original size:18 final size:18
Alignment explanation
Indices: 1118342--1118376 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1118332 CAAACGTATC
1118342 TTTTTATAATATTTATAT
1 TTTTTATAATATTTATAT
*
1118360 TTTTTATAATGTTTATA
1 TTTTTATAATATTTATA
1118377 AAATAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTTATAATATTTATAT
Found at i:1121375 original size:17 final size:16
Alignment explanation
Indices: 1121349--1121401 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
1121339 GATGAGTTTT
1121349 AAAAAATATTTTTTAA
1 AAAAAATATTTTTTAA
1121365 AAAAAATTATTTTTTAA
1 AAAAAA-TATTTTTTAA
***
1121382 TTTAAATATTTTTTAA
1 AAAAAATATTTTTTAA
1121398 AAAA
1 AAAA
1121402 TAGTTTGACT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAAAATATTTTTTAA
Found at i:1124041 original size:26 final size:25
Alignment explanation
Indices: 1123987--1124041 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 25
1123977 ACCTGACCCC
*
1123987 GACTCGATATCACACTAAAAAAACCT
1 GACTCGATATCAAACTAAAAAAA-CT
1124013 GACTCGAATATCAAACTTAAAAAAA-T
1 GACTCG-ATATCAAAC-TAAAAAAACT
1124039 GAC
1 GAC
1124042 CCGACCTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 10 0.38
27 8 0.31
28 8 0.31
ACGTcount: A:0.49, C:0.22, G:0.09, T:0.20
Consensus pattern (25 bp):
GACTCGATATCAAACTAAAAAAACT
Found at i:1124531 original size:22 final size:20
Alignment explanation
Indices: 1124481--1124531 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 20
1124471 TTTATGTCTG
1124481 TTTTAT-AAAAATAATTTAT
1 TTTTATAAAAAATAATTTAT
1124500 TTGTTAATAAAAAATAAATTTTAT
1 TT-TT-ATAAAAAAT-AA-TTTAT
1124524 TTTTATAA
1 TTTTATAA
1124532 TTATTTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 2 0.07
20 2 0.07
21 2 0.07
22 10 0.37
23 4 0.15
24 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTTATAAAAAATAATTTAT
Found at i:1129659 original size:2 final size:2
Alignment explanation
Indices: 1129652--1129677 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1129642 GTGAAAGATT
1129652 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
1129678 AACCCTAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1132611 original size:22 final size:22
Alignment explanation
Indices: 1132578--1132629 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
1132568 TAACTCACAC
1132578 ATTTA-TTTAAATTTAAAT-TTT
1 ATTTATTTTAAA-TTAAATATTT
1132599 ATTTATTTTAAATTAAATAATTT
1 ATTTATTTTAAATTAAAT-ATTT
1132622 ATTT-TTTT
1 ATTTATTTT
1132630 CATAGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 11 0.39
22 10 0.36
23 7 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTATTTTAAATTAAATATTT
Found at i:1133596 original size:28 final size:29
Alignment explanation
Indices: 1133565--1133621 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
1133555 TGAGTGAAAT
*
1133565 TAGACTTTTT-TTTGGAAGAGTCATTTAC
1 TAGACTTTTTCTTTGGAAAAGTCATTTAC
1133593 TAGACTTTTTCCTTTGGAAAAGTCATTTA
1 TAGACTTTTT-CTTTGGAAAAGTCATTTA
1133622 TTGATAGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 10 0.38
30 16 0.62
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (29 bp):
TAGACTTTTTCTTTGGAAAAGTCATTTAC
Found at i:1134530 original size:17 final size:16
Alignment explanation
Indices: 1134510--1134542 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1134500 ATACACATTC
1134510 ATATTATAAATATTATT
1 ATATTATAAA-ATTATT
1134527 ATATTATAAAATTATT
1 ATATTATAAAATTATT
1134543 TAGTGAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATTATAAAATTATT
Found at i:1138336 original size:6 final size:6
Alignment explanation
Indices: 1138327--1138355 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1138317 CAAGGAGGAC
1138327 AATGTG AATGTG AATGTG AATGTG AATGT
1 AATGTG AATGTG AATGTG AATGTG AATGT
1138356 CGGATATCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (6 bp):
AATGTG
Found at i:1140721 original size:12 final size:12
Alignment explanation
Indices: 1140704--1140729 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1140694 AGGTGCCTAG
1140704 CCGTTAGTTTTT
1 CCGTTAGTTTTT
1140716 CCGTTAGTTTTT
1 CCGTTAGTTTTT
1140728 CC
1 CC
1140730 TGTAAGTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.23, G:0.15, T:0.54
Consensus pattern (12 bp):
CCGTTAGTTTTT
Found at i:1140774 original size:22 final size:24
Alignment explanation
Indices: 1140747--1140795 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1140737 GACAAAAAAA
1140747 ATAAAATATT-AAAA-AAAATTAT
1 ATAAAATATTAAAAATAAAATTAT
1140769 ATAAAATATTAAAAATAAAATTAT
1 ATAAAATATTAAAAATAAAATTAT
1140793 ATA
1 ATA
1140796 TTTTTAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 10 0.40
23 4 0.16
24 11 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAAATATTAAAAATAAAATTAT
Found at i:1140789 original size:14 final size:12
Alignment explanation
Indices: 1140745--1140781 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
1140735 GTGACAAAAA
1140745 AAATAAAATATT
1 AAATAAAATATT
1140757 AAA-AAAA-ATT
1 AAATAAAATATT
*
1140767 ATATAAAATATT
1 AAATAAAATATT
1140779 AAA
1 AAA
1140782 AATAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 5 0.24
11 8 0.38
12 8 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATAAAATATT
Found at i:1142686 original size:16 final size:16
Alignment explanation
Indices: 1142651--1142688 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1142641 TTATTTTATT
*
1142651 ATGTTTCTTAATAGAT
1 ATGTTTCTTAATAGAA
1142667 ATGTTTCTTAAT-GAAA
1 ATGTTTCTTAATAG-AA
1142683 ATGTTT
1 ATGTTT
1142689 TTTTTTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (16 bp):
ATGTTTCTTAATAGAA
Found at i:1143105 original size:32 final size:33
Alignment explanation
Indices: 1143064--1143127 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 33
1143054 TTATTTTGAT
1143064 TTTGCTCCCCCCA-TTTATTATTATTAATTATAG
1 TTTGCT-CCCCCATTTTATTATTATTAATTATAG
* * *
1143097 TTTG-TCCCCTATTTTTTTATTGTTAATTATA
1 TTTGCTCCCCCATTTTATTATTATTAATTATA
1143128 TTTTACCTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 5 0.19
32 18 0.67
33 4 0.15
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.55
Consensus pattern (33 bp):
TTTGCTCCCCCATTTTATTATTATTAATTATAG
Found at i:1162138 original size:34 final size:34
Alignment explanation
Indices: 1162095--1162180 Score: 163
Period size: 34 Copynumber: 2.5 Consensus size: 34
1162085 TACTTGGATT
1162095 TCAACTTCACGGCGAAGGATATTCAAGTCAAGGC
1 TCAACTTCACGGCGAAGGATATTCAAGTCAAGGC
1162129 TCAACTTCACGGCGAAGGATATTCAAGTCAAGGC
1 TCAACTTCACGGCGAAGGATATTCAAGTCAAGGC
*
1162163 TCAACTTCACGACGAAGG
1 TCAACTTCACGGCGAAGG
1162181 GGCCATCCGC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (34 bp):
TCAACTTCACGGCGAAGGATATTCAAGTCAAGGC
Found at i:1162481 original size:99 final size:99
Alignment explanation
Indices: 1162312--1162611 Score: 361
Period size: 106 Copynumber: 3.0 Consensus size: 99
1162302 AATTTCATAA
* *
1162312 CCAATTTCAACTTCACAGCGAAGGATATTGGA-TCCAAGACAACACAAGCCCAACTTCACGACGA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACT-CAAGACAACACAAGCTCAACTTCACGGCGA
* ** *
1162376 AAGGGCGGTTGATTGTCAACAAACAATTTTCAGAGT
65 AGGGGCGACTGACTGTCAACAAACAATTTTCAGA-T
* * *
1162412 -CAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACATCACAAGCTCAACTTCACGGCGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACGGCGAA
*
1162476 GGGGCGACTGACTATCAACAAACAATTCCCCAATTTCAGAT
66 GGGGCGACTGACTGTCAACAAACAA-T------TTTCAGAT
* * * * *
1162517 CCAATTTCACCTTCACAGCGAATGATATTGGACCCAAGACAGCACAAGCTCAACTTCACGGTGAA
1 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACGGCGAA
*
1162582 GGGGCGACTGACTGTCAACAAATAATTTTC
66 GGGGCGACTGACTGTCAACAAACAATTTTC
1162612 CAGTTCCAGA
Statistics
Matches: 172, Mismatches: 19, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
99 81 0.47
100 2 0.01
105 2 0.01
106 87 0.51
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (99 bp):
CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACGGCGAA
GGGGCGACTGACTGTCAACAAACAATTTTCAGAT
Found at i:1162557 original size:106 final size:106
Alignment explanation
Indices: 1162403--1162655 Score: 339
Period size: 106 Copynumber: 2.4 Consensus size: 106
1162393 AACAAACAAT
* * * *
1162403 TTTCAGAGT-CAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACATCACAAGCTCAACTT
1 TTTCAGA-TCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTT
1162467 CACGGCGAAGGGGCGACTGACTATCAACAAACAATTCCCCAA
65 CACGGCGAAGGGGCGACTGACTATCAACAAACAATTCCCCAA
* *
1162509 TTTCAGATCCAATTTCACCTTCACAGCGAATGATATTGGACCCAAGACAGCACAAGCTCAACTTC
1 TTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTC
* * * ** *
1162574 ACGGTGAAGGGGCGACTGACTGTCAACAAATAATTTTCCAG
66 ACGGCGAAGGGGCGACTGACTATCAACAAACAATTCCCCAA
* * *
1162615 TTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGAC
1 TTTCAGATCCAATTTCAACTTCACAG-CGAAGGATATTGGAC
1162656 TCGGAGCAGT
Statistics
Matches: 128, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
105 2 0.02
106 126 0.98
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (106 bp):
TTTCAGATCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTC
ACGGCGAAGGGGCGACTGACTATCAACAAACAATTCCCCAA
Found at i:1168740 original size:38 final size:38
Alignment explanation
Indices: 1168686--1168877 Score: 276
Period size: 38 Copynumber: 5.1 Consensus size: 38
1168676 GTTCTTTGTA
* *
1168686 TGGATGATATTCTGTCATGCACATACCATGCTCGGATT
1 TGGATGATATTGTGTCATGCGCATACCATGCTCGGATT
* * *
1168724 TGGATGATATTGTGTCACGTGGATACCATGCTCGGATT
1 TGGATGATATTGTGTCATGCGCATACCATGCTCGGATT
* * *
1168762 TCGATGATATTGTGTCACGTGCATACCATGCTCGGATT
1 TGGATGATATTGTGTCATGCGCATACCATGCTCGGATT
* * *
1168800 TGGATGATATTGTGTCATGTGAATACCATGCTTGGATT
1 TGGATGATATTGTGTCATGCGCATACCATGCTCGGATT
*
1168838 TGGATGATATTATGTCATGCGCATACCATGCTCGGATT
1 TGGATGATATTGTGTCATGCGCATACCATGCTCGGATT
1168876 TG
1 TG
1168878 TTCTAGAACC
Statistics
Matches: 139, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 139 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.35
Consensus pattern (38 bp):
TGGATGATATTGTGTCATGCGCATACCATGCTCGGATT
Found at i:1169968 original size:2 final size:2
Alignment explanation
Indices: 1169961--1170011 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1169951 TAGGTAATTA
1169961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1170003 AT AT AT AT A
1 AT AT AT AT A
1170012 GAAGATTTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1175887 original size:27 final size:27
Alignment explanation
Indices: 1175849--1175910 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
1175839 TGACATTAGA
1175849 TTCAGTTCGGGTTCAGGTCGGGTTAAT
1 TTCAGTTCGGGTTCAGGTCGGGTTAAT
1175876 TTCAGTTCGGGTTCAGGTCGGGTTAAT
1 TTCAGTTCGGGTTCAGGTCGGGTTAAT
1175903 TTCAGTTC
1 TTCAGTTC
1175911 AGATCGATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.15, C:0.16, G:0.31, T:0.39
Consensus pattern (27 bp):
TTCAGTTCGGGTTCAGGTCGGGTTAAT
Found at i:1175906 original size:16 final size:16
Alignment explanation
Indices: 1175860--1175907 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
1175850 TCAGTTCGGG
1175860 TTCAGGTCGGGTTAAT
1 TTCAGGTCGGGTTAAT
*
1175876 TTCAGTTCGGG-----
1 TTCAGGTCGGGTTAAT
1175887 TTCAGGTCGGGTTAAT
1 TTCAGGTCGGGTTAAT
1175903 TTCAG
1 TTCAG
1175908 TTCAGATCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
11 10 0.40
16 15 0.60
ACGTcount: A:0.17, C:0.15, G:0.31, T:0.38
Consensus pattern (16 bp):
TTCAGGTCGGGTTAAT
Found at i:1176455 original size:14 final size:13
Alignment explanation
Indices: 1176436--1176470 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
1176426 ATTAAATTGA
1176436 ATAAATATAAAATT
1 ATAAATA-AAAATT
1176450 ATAAATAAAAATT
1 ATAAATAAAAATT
1176463 -TAAATAAA
1 ATAAATAAA
1176471 TTAAAGAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.38
13 6 0.29
14 7 0.33
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAATAAAAATT
Found at i:1176587 original size:2 final size:2
Alignment explanation
Indices: 1176582--1176865 Score: 129
Period size: 2 Copynumber: 144.5 Consensus size: 2
1176572 AACAATGATA
*
1176582 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1176624 AT -T AT AT A- AG AA AT AT AT AT AT AT AGT AT AT AT AT AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT
* * * *
1176666 AT GAT TT AT AT AT AGT TT AT A- AT A- AT AA ACT AT AT A- AT TT
1 AT -AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT
* * *
1176706 AT AT AT AGT AT AT AT A- AT TT AT A- AT -T AT AC CT AGT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * * *
1176747 AT -T A- AT AT CAG CT AT AT AT A- AT CAG CT AT AT AT AT AA AT -T
1 AT AT AT AT AT -AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
*
1176787 AT AT AT ACT AT AT AGT -T GAT AT -T A- AT AT AT AT AT ACT AT GT
1 AT AT AT A-T AT AT A-T AT -AT AT AT AT AT AT AT AT AT A-T AT AT
* * *
1176828 AT A- AT -T AT AA AT -T AT AT AT ACT AT CT AT AA AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A
1176866 GTTTAGTAAT
Statistics
Matches: 211, Mismatches: 38, Indels: 66
0.67 0.12 0.21
Matches are distributed among these distances:
1 19 0.09
2 171 0.81
3 21 0.10
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1176960 original size:72 final size:77
Alignment explanation
Indices: 1176833--1177001 Score: 178
Period size: 72 Copynumber: 2.3 Consensus size: 77
1176823 TATGTATAAT
* *
1176833 TATAAATTATATAT--ACTATCTATAAATTATATAGTTTAGTAATATAAACTCTATAT-A-TA-A
1 TATAAATTATATATAAACTA--TATAAACTATATAGTTTAGTAATATAAACTATATATAATTATA
*
1176893 AA-TA-ATAGACTA
64 AATTATATAAACTA
* * *
1176905 TATAAATTATATATAAACTATATAAACTGTATAGTTTA-TATTTATACACTATATATAATTATAA
1 TATAAATTATATATAAACTATATAAACTATATAGTTTAGTA-ATATAAACTATATATAATTATAA
1176969 ATTATATAAACTA
65 ATTATATAAACTA
*
1176982 TAT--TTTATATATAAACTATA
1 TATAAATTATATATAAACTATA
1177002 GTCTATATAT
Statistics
Matches: 82, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
71 2 0.02
72 42 0.51
73 1 0.01
74 6 0.07
75 19 0.23
76 2 0.02
77 10 0.12
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.43
Consensus pattern (77 bp):
TATAAATTATATATAAACTATATAAACTATATAGTTTAGTAATATAAACTATATATAATTATAAA
TTATATAAACTA
Found at i:1176961 original size:24 final size:26
Alignment explanation
Indices: 1176916--1176984 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 26
1176906 ATAAATTATA
* *
1176916 TATAAACTATATAAACTGTATAGT--T
1 TATAAATTATATAAACTATATA-TAAT
*
1176941 TAT--ATT-TATACACTATATATAAT
1 TATAAATTATATAAACTATATATAAT
1176964 TATAAATTATATAAACTATAT
1 TATAAATTATATAAACTATAT
1176985 TTTATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 11 0.31
23 6 0.17
25 6 0.17
26 11 0.31
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (26 bp):
TATAAATTATATAAACTATATATAAT
Found at i:1176994 original size:18 final size:18
Alignment explanation
Indices: 1176971--1177020 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
1176961 AATTATAAAT
* *
1176971 TATATAAACTATATTTTA
1 TATATAAACTATAGTCTA
1176989 TATATAAACTATAGTCTA
1 TATATAAACTATAGTCTA
1177007 TATATAAACTATAG
1 TATATAAACTATAG
1177021 AGTTTTACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (18 bp):
TATATAAACTATAGTCTA
Done.